Friday, November 30, 2007

Tuesday, November 27, 2007

Charles Darwin called the evolution of flowering plants an "abominable mystery." Recent research has shown that flowering plants suddenly appeared in yet another "big bang" for evolution. A recent press release published at ScienceDaily, reports as follows:

Doug and Pam Soltis, a UF professor of botany and curator at UF's Florida Museum of Natural History, respectively, also showed that a stunning diversification of flowering plants they are referring to as the "Big Bang" took place in the comparatively short period of less than 5 million years -- and resulted in all five major lineages of flowering plants that exist today."Flowering plants today comprise around 400,000 species," said Pam Soltis. "So to think that the burst that give rise to almost all of these plants occurred in less than 5 million years is pretty amazing -- especially when you consider that flowering plants as a group have been around for at least 130 million years.[emphasis mine]

I should point out that it is also possible that flowers appeared in a much smaller time frame but the resolution of the fossil record is only able to narrow it to 5 million years. However, in evolutionary years, 5 million years is plenty quick.

The press release has more to say.

Jansen and his UT Austin colleagues analyzed DNA sequences of 81 genes from the chloroplast genome of 64 plant species, while the UF researchers analyzed 61 genes from 45 species. The two groups also performed a combined analysis, which produced evolutionary trees that included all the major groups of flowering plants.The analyses also confirmed that a unique species of plant called Amborella, found only on the Pacific island of New Caledonia, represents the earliest diverging lineage of flowering plants.By laboriously arranging the sequences, the researchers slowly built a kind of family tree for plants -- a diagram of relationships among plant lineages showing diversification over the eons. Based on known rates of genetic change double-checked against fossils of known ages, they established a time scale that revealed the dates of major branching events.

This should be taken with a healthy dose of skepticism. Phylogenetic trees are based on the assumption that such a tree exists to begin with. Different genes often yield "alternative conflicting phylogenies." (Carroll & Rokas)

Can we realistically hope to resolve diversification events spanning a few or even tens of millions of years that occurred in deep time? It is widely accepted that nucleotide data are of limited use for resolving deep divergences because of mutational saturation and homoplasy. Until the recent expansion in available data, it has not been possible to fully explore what the limits of the protein record might be. Like others in the field, we also had expectations that scaling up dataset size would be sufficient to resolve interesting groups. The evidence presented here suggests that large amounts of conventional characters will not always suffice, even if analyzed by state-of-the-art methodology. Just as it would be futile to use radioisotopes with modest half lives to date ancient rocks, it appears unrealistic to expect conventional linear, homoplasy-sensitive sequences to reliably resolve series of events that transpired in a small fraction of deep time. (Carroll and Rokas) [emphasis mine]

Yet this recent research purposes to do exactly that, resolve a series of events that transpired in a small fraction of deep time. What's more they do it by only examining the chloroplast genome, increasing the subjectivity of the excercise. The press release continues:

By laboriously arranging the sequences, the researchers slowly built a kind of family tree for plants -- a diagram of relationships among plant lineages showing diversification over the eons. Based on known rates of genetic change double-checked against fossils of known ages, they established a time scale that revealed the dates of major branching events.

So now molecular clocks are thrown into the mix to establish the times of the already suspect divergences. Is that accurate? Not really. Molecular clocks are mostly based upon circular logic and are often wildley subjective, as a recent peer review article entitled "Dates from the molecular clock: how wrong can we be?" by Mário J.F. Pulquério and Richard A. Nichols explains

Large discrepancies have been found in dates of evolutionary events obtained using the molecular clock. Twofold differences have been reported between the dates estimated from molecular data and those from the fossil record; furthermore, different molecular methods can give dates that differ 20-fold. New software attempts to incorporate appropriate allowances for this uncertainty into the calculation of the accuracy of date estimates. Here, we propose that these innovations represent welcome progress towards obtaining reliable dates from the molecular clock, but warn that they are currently unproven, given that the causes and pattern of the discrepancies are the subject of ongoing research. ... We currently do not know enough to be confident in the prospects of these new methods, and some initial results are discouraging.

What is really interesting about the research, and why I post it here, is that points out how poorly Darwinism is able to explain the "abominable mystery" of flowers. There is really no clue as to how are why such beautiful variety could appear so quickly. The press release explains:

The latest research clears the picture by showing that all plants fall into five major lineages that developed over the relatively short period of 5 million years, or possibly even less.

As for the diversification's cause, it remains mysterious, Pam and Doug Soltis said.[emphasis mine]